Uncontrolled applications of weedicide and fertilizer can harm the soil ecology, and most significantly, earthworms are hazardous soil engineers. Thus, we aimed at the toxicity and histopathological alterations in the earthworm Eudrilus euginae following exposure to glyphosate (weedicide), urea (fertilizer), and environmentally friendly dual herb-mixed silver nanoparticles (DHM-AgNPs). The DHM-AgNPs were synthesized using a blend of Alfinia officinarum and Curcuma longa aqueous leaf extracts with 1 mM silver nitrate. The color change from yellow to brown after an hour of incubation was a significant indicator of successful DHM-AgNP synthesis. Characterization of the DHM-AgNPs using UV–Vis spectra indicated a surface plasmon resonance (SPR) peak at 430 nm. In addition to FT-IR spectroscopy and XRD analysis, SEM, TEM, and SEM investigations were performed to identify the DHM-AgNPs. The XPS analysis revealed the oxidation state and surface chemical composition, and Ag NP's specific surface area and degree of porosity were measured using BET. Furthermore, different concentrations of urea and glyphosate were administered to Artemia nauplii and E. euginae to assess their toxicity. The mortality rate for E. euginae exposed to a higher urea concentration (10 g/kg of soil) was 100%. In contrast, a % mortality rate of 83% was noted at 0.5 g/kg of soil. The maximum mortality (90 ± 0.64%) was observed at a 10 mL/kg/L concentration for glyphosate. In contrast, low mortality was noted in E. euginae and A. nauplii exposed with gradient concentrations of DHM-AgNPs compared to glyphosate and urea. As aquaculture and foodborne diseases are widespread, DHM-AgNPs showed significant anti-Vibrio activity against pathogenic Vibrio-related bacteria, inhibiting 80% at 100,100 μg/L, which is of great concern. This study suggests the potential use of DHM-AgNPs in field aqua and crops culture for eco-friendly pest control and anti-Vibrio activity without causing soil and environmental pollution. Further research is warranted to determine the efficacy, safety, and cost-effectiveness of DHM-AgNPs in aqua and agricultural practices.